Atomistry » Zinc » PDB 4eez-4eyf » 4eg2
Atomistry »
  Zinc »
    PDB 4eez-4eyf »
      4eg2 »

Zinc in PDB 4eg2: 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine

Enzymatic activity of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine

All present enzymatic activity of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine:
3.5.4.5;

Protein crystallography data

The structure of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine, PDB code: 4eg2 was solved by G.Minasov, Z.Wawrzak, T.Skarina, Y.Wang, S.Grimshaw, L.Papazisi, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.21 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.810, 163.730, 111.950, 90.00, 97.70, 90.00
R / Rfree (%) 15.9 / 21

Other elements in 4eg2:

The structure of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine (pdb code 4eg2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine, PDB code: 4eg2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 1 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:36.3
occ:0.25
 SG A:CYS132 2.1 26.8 1.0
SG A:CYS129 2.2 25.2 1.0
ND1 A:HIS102 2.4 23.6 1.0
O4 A:URI302 2.8 36.0 1.0
CE1 A:HIS102 2.9 27.8 1.0
C4 A:URI302 3.0 32.3 1.0
CB A:CYS132 3.1 22.3 1.0
CG A:HIS102 3.3 23.1 1.0
CB A:CYS129 3.4 23.0 1.0
N3 A:URI302 3.5 31.1 1.0
C5 A:URI302 3.5 34.2 1.0
N A:CYS132 3.6 20.8 1.0
N A:CYS129 3.6 22.6 1.0
CA A:CYS132 3.9 21.4 1.0
CB A:HIS102 3.9 19.7 1.0
NE2 A:HIS102 4.0 24.4 1.0
CA A:CYS129 4.0 22.9 1.0
OE1 A:GLU104 4.1 17.6 1.0
CD2 A:HIS102 4.2 26.2 1.0
O A:CYS129 4.3 19.9 1.0
C6 A:URI302 4.3 32.5 1.0
C A:CYS129 4.4 21.4 1.0
C2 A:URI302 4.4 31.5 1.0
CD A:GLU104 4.5 25.3 1.0
OE2 A:GLU104 4.5 28.8 1.0
CD2 A:HIS131 4.5 19.8 1.0
C A:HIS131 4.7 20.6 1.0
C A:PRO128 4.7 23.9 1.0
N1 A:URI302 4.7 31.2 1.0
CB A:HIS131 4.8 19.3 1.0
CA A:PRO128 4.9 24.8 1.0

Zinc binding site 2 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 2 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:34.2
occ:0.25
 SG B:CYS129 2.2 28.9 1.0
ND1 B:HIS102 2.3 23.1 1.0
SG B:CYS132 2.4 26.0 1.0
CE1 B:HIS102 2.9 26.0 1.0
O4 B:URI303 3.1 37.5 1.0
C4 B:URI303 3.1 37.1 1.0
CG B:HIS102 3.2 19.6 1.0
CB B:CYS132 3.3 23.1 1.0
CB B:CYS129 3.5 25.8 1.0
N B:CYS132 3.5 22.7 1.0
C5 B:URI303 3.5 37.5 1.0
N3 B:URI303 3.6 35.6 1.0
N B:CYS129 3.7 25.3 1.0
CB B:HIS102 3.8 19.6 1.0
NE2 B:HIS102 3.8 22.7 1.0
CA B:CYS132 3.9 22.3 1.0
CD2 B:HIS102 4.0 23.8 1.0
CA B:CYS129 4.0 25.5 1.0
CD2 B:HIS131 4.1 23.1 1.0
C6 B:URI303 4.3 37.8 1.0
O B:CYS129 4.3 22.4 1.0
C B:CYS129 4.4 23.2 1.0
C2 B:URI303 4.4 36.1 1.0
CB B:HIS131 4.4 22.6 1.0
OE1 B:GLU104 4.5 25.5 1.0
C B:HIS131 4.5 21.1 1.0
CG B:HIS131 4.6 22.6 1.0
N1 B:URI303 4.6 36.4 1.0
C B:PRO128 4.8 26.9 1.0
CD B:GLU104 4.8 27.9 1.0
N B:HIS131 4.9 21.1 1.0
CA B:HIS131 4.9 20.9 1.0
OE2 B:GLU104 4.9 29.5 1.0

Zinc binding site 3 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 3 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:32.6
occ:0.25
 SG C:CYS132 2.2 27.5 1.0
ND1 C:HIS102 2.3 24.0 1.0
SG C:CYS129 2.3 33.7 1.0
O4 C:URI302 2.8 42.3 1.0
CE1 C:HIS102 2.9 23.6 1.0
C4 C:URI302 2.9 42.2 1.0
CB C:CYS132 3.1 22.7 1.0
CG C:HIS102 3.2 20.1 1.0
N3 C:URI302 3.4 40.7 1.0
C5 C:URI302 3.5 42.1 1.0
CB C:CYS129 3.6 27.6 1.0
N C:CYS132 3.7 22.0 1.0
N C:CYS129 3.7 26.6 1.0
CB C:HIS102 3.8 19.1 1.0
NE2 C:HIS102 3.9 21.0 1.0
CA C:CYS132 4.0 22.0 1.0
CD2 C:HIS102 4.1 18.8 1.0
CA C:CYS129 4.1 27.6 1.0
OE1 C:GLU104 4.2 28.6 1.0
C2 C:URI302 4.2 42.0 1.0
C6 C:URI302 4.3 44.9 1.0
CD2 C:HIS131 4.3 28.7 1.0
O C:CYS129 4.4 23.7 1.0
C C:CYS129 4.5 25.4 1.0
CD C:GLU104 4.6 28.0 1.0
N1 C:URI302 4.6 43.1 1.0
OE2 C:GLU104 4.6 30.8 1.0
CB C:HIS131 4.7 22.2 1.0
C C:HIS131 4.8 22.3 1.0
C C:PRO128 4.8 27.7 1.0
CG C:HIS131 4.9 25.1 1.0
CA C:PRO128 5.0 29.1 1.0

Zinc binding site 4 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 4 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:32.9
occ:0.25
 SG D:CYS132 2.2 28.0 1.0
ND1 D:HIS102 2.2 23.9 1.0
SG D:CYS129 2.4 27.2 1.0
CE1 D:HIS102 2.8 25.3 1.0
O4 D:URI302 2.9 37.3 1.0
C4 D:URI302 3.0 35.6 1.0
CG D:HIS102 3.1 23.5 1.0
CB D:CYS132 3.2 22.0 1.0
N3 D:URI302 3.3 34.4 1.0
C5 D:URI302 3.5 34.6 1.0
CB D:CYS129 3.6 23.6 1.0
N D:CYS132 3.7 21.3 1.0
CB D:HIS102 3.7 20.6 1.0
N D:CYS129 3.7 23.4 1.0
NE2 D:HIS102 3.8 20.2 1.0
CD2 D:HIS102 4.0 23.7 1.0
CA D:CYS132 4.0 21.7 1.0
CA D:CYS129 4.1 23.4 1.0
C2 D:URI302 4.1 35.2 1.0
C6 D:URI302 4.2 33.6 1.0
OE1 D:GLU104 4.3 23.4 1.0
CD2 D:HIS131 4.4 29.5 1.0
O D:CYS129 4.5 18.1 1.0
OE2 D:GLU104 4.5 28.6 1.0
N1 D:URI302 4.5 34.3 1.0
C D:CYS129 4.5 21.2 1.0
CD D:GLU104 4.6 29.8 1.0
CB D:HIS131 4.6 23.0 1.0
C D:HIS131 4.7 22.4 1.0
C D:PRO128 4.8 25.2 1.0
O2 D:URI302 4.9 29.4 1.0
CG D:HIS131 4.9 25.6 1.0

Zinc binding site 5 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 5 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:36.6
occ:0.25
 SG E:CYS132 2.0 31.2 1.0
ND1 E:HIS102 2.3 25.3 1.0
SG E:CYS129 2.3 33.6 1.0
O4 E:URI302 2.7 40.5 1.0
C4 E:URI302 2.8 39.8 1.0
CE1 E:HIS102 3.0 25.6 1.0
CB E:CYS132 3.0 26.5 1.0
CG E:HIS102 3.1 24.1 1.0
N3 E:URI302 3.2 40.2 1.0
C5 E:URI302 3.4 40.4 1.0
N E:CYS132 3.6 24.9 1.0
CB E:CYS129 3.6 30.5 1.0
CB E:HIS102 3.7 22.9 1.0
N E:CYS129 3.8 29.7 1.0
CA E:CYS132 3.8 24.9 1.0
NE2 E:HIS102 3.9 23.5 1.0
CD2 E:HIS102 4.0 23.8 1.0
C2 E:URI302 4.1 40.0 1.0
C6 E:URI302 4.2 39.8 1.0
CA E:CYS129 4.2 29.8 1.0
OE1 E:GLU104 4.2 24.8 1.0
CD2 E:HIS131 4.2 27.3 1.0
N1 E:URI302 4.5 40.4 1.0
O E:CYS129 4.5 26.5 1.0
CD E:GLU104 4.5 31.7 1.0
C E:CYS129 4.5 27.2 1.0
CB E:HIS131 4.6 26.7 1.0
OE2 E:GLU104 4.6 35.8 1.0
C E:HIS131 4.6 24.0 1.0
CG E:HIS131 4.8 27.3 1.0
O2 E:URI302 4.9 37.4 1.0
C E:PRO128 4.9 29.9 1.0

Zinc binding site 6 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 6 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:40.4
occ:0.25
 SG F:CYS129 2.0 27.9 1.0
SG F:CYS132 2.3 30.3 1.0
ND1 F:HIS102 2.6 27.1 1.0
O4 F:URI302 3.0 26.9 1.0
CE1 F:HIS102 3.1 29.0 1.0
CB F:CYS132 3.1 22.8 1.0
C4 F:URI302 3.1 27.0 1.0
CB F:CYS129 3.2 26.4 1.0
N F:CYS129 3.4 25.5 1.0
N F:CYS132 3.4 24.1 1.0
CG F:HIS102 3.6 23.9 1.0
C5 F:URI302 3.6 28.4 1.0
CA F:CYS129 3.7 25.4 1.0
N3 F:URI302 3.7 27.7 1.0
CA F:CYS132 3.8 23.4 1.0
O F:CYS129 3.9 22.3 1.0
C F:CYS129 4.0 22.9 1.0
NE2 F:HIS102 4.1 25.4 1.0
CB F:HIS102 4.2 21.6 1.0
CB F:HIS131 4.3 25.2 1.0
C6 F:URI302 4.4 30.2 1.0
CD2 F:HIS102 4.4 25.6 1.0
C F:HIS131 4.4 24.6 1.0
CD2 F:HIS131 4.5 32.2 1.0
C F:PRO128 4.5 27.3 1.0
C2 F:URI302 4.6 28.0 1.0
N F:HIS131 4.6 23.4 1.0
OE1 F:GLU104 4.7 23.7 1.0
CA F:HIS131 4.7 25.0 1.0
OE2 F:GLU104 4.7 33.8 1.0
CG F:HIS131 4.8 27.3 1.0
CD F:GLU104 4.8 29.3 1.0
N1 F:URI302 4.8 29.2 1.0
CA F:PRO128 4.9 28.4 1.0
N F:GLY130 4.9 21.4 1.0

Zinc binding site 7 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 7 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:40.8
occ:0.25
 SG G:CYS132 2.1 34.9 1.0
ND1 G:HIS102 2.2 30.5 1.0
SG G:CYS129 2.4 36.2 1.0
CE1 G:HIS102 2.8 29.0 1.0
CG G:HIS102 3.0 26.7 1.0
C4 G:URI302 3.0 43.4 1.0
O4 G:URI302 3.0 45.4 1.0
CB G:CYS132 3.1 28.8 1.0
N3 G:URI302 3.4 43.8 1.0
C5 G:URI302 3.5 45.5 1.0
CB G:HIS102 3.6 24.6 1.0
NE2 G:HIS102 3.6 28.3 1.0
N G:CYS132 3.7 29.1 1.0
CB G:CYS129 3.7 30.4 1.0
CD2 G:HIS102 3.7 27.7 1.0
N G:CYS129 3.8 31.3 1.0
CA G:CYS132 3.9 29.0 1.0
CD2 G:HIS131 4.0 33.8 1.0
OE1 G:GLU104 4.1 24.6 1.0
C2 G:URI302 4.2 42.6 1.0
C6 G:URI302 4.2 44.5 1.0
CA G:CYS129 4.2 31.7 1.0
N1 G:URI302 4.5 42.8 1.0
O G:CYS129 4.5 31.4 1.0
CD G:GLU104 4.6 31.5 1.0
CB G:HIS131 4.6 30.9 1.0
C G:CYS129 4.6 32.0 1.0
C G:HIS131 4.6 29.9 1.0
CG G:HIS131 4.7 33.4 1.0
OE2 G:GLU104 4.7 35.0 1.0
C G:PRO128 4.9 32.3 1.0
O2 G:URI302 4.9 35.4 1.0

Zinc binding site 8 out of 8 in 4eg2

Go back to Zinc Binding Sites List in 4eg2
Zinc binding site 8 out of 8 in the 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:50.3
occ:0.25
 SG H:CYS132 2.1 35.9 1.0
SG H:CYS129 2.2 41.0 1.0
ND1 H:HIS102 2.4 28.2 1.0
O4 H:URI302 2.7 59.3 1.0
C4 H:URI302 2.9 62.7 1.0
CE1 H:HIS102 3.0 31.4 1.0
CB H:CYS132 3.0 27.6 1.0
CG H:HIS102 3.3 28.6 1.0
N3 H:URI302 3.4 62.0 1.0
C5 H:URI302 3.4 63.8 1.0
N H:CYS129 3.5 33.1 1.0
CB H:CYS129 3.5 33.8 1.0
N H:CYS132 3.6 27.3 1.0
CA H:CYS132 3.9 27.3 1.0
CB H:HIS102 3.9 28.7 1.0
CA H:CYS129 3.9 33.8 1.0
NE2 H:HIS102 4.0 29.0 1.0
O H:CYS129 4.2 30.1 1.0
CD2 H:HIS102 4.2 28.3 1.0
C6 H:URI302 4.3 63.9 1.0
C2 H:URI302 4.3 63.3 1.0
OE1 H:GLU104 4.3 32.4 1.0
C H:CYS129 4.3 31.7 1.0
OE2 H:GLU104 4.4 38.3 1.0
CD2 H:HIS131 4.4 30.1 1.0
CD H:GLU104 4.5 35.4 1.0
C H:PRO128 4.6 34.4 1.0
CB H:HIS131 4.6 27.2 1.0
N1 H:URI302 4.6 64.7 1.0
C H:HIS131 4.7 26.2 1.0
CA H:PRO128 4.8 35.6 1.0
CG H:HIS131 4.9 30.1 1.0

Reference:

G.Minasov, Z.Wawrzak, T.Skarina, Y.Wang, S.Grimshaw, L.Papazisi, A.Savchenko, W.F.Anderson. 2.2 Angstrom Crystal Structure of Cytidine Deaminase From Vibrio Cholerae in Complex with Zinc and Uridine. To Be Published.
Page generated: Sat Oct 26 22:00:11 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy